Clarke dropped to the bench despite his outstanding performance in the second leg of the semi final against Sheffield Wednesday, but came on to make a significant contribution in the latter stages as Sunderland secured a place in the Championship.
Neil said he had made the selection after watching the two regular season fixtures between the sides, in which the 23-year-old had thrived.
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"I watched the last two games against Wycombe and Elliot Embleton was unbelievable in both games," said Neil.
"He created a goal for Ross Stewart who scored a header, there was a throw-in and he played a one-two and banged it in the far corner, created one down at their place which Ross scored, and he also hit the underside of the bar. There are certain players who suit playing specific teams.
"It was a brave decision today because I'm sure there would be people there asking why Jack Clarke wasn't playing, but then Embo did exactly what I thought he would do - that he would have a key moment in the game, and he did.
"It's not fortune, because there's a lot of hard work that goes into it.
"When it works and it happens, it's so pleasing because I thought he would have that impact and he did."
Embleton spoke to Sky Sports after the game and said it was an 'unbelievable' feeling.
It was his second consecutive promotion from League One in the play-off final after his hugely successful loan at Blackpool last year.
"It's unbelievable, I've been here since I was seven so to win at Wembley in front of 50,000 Sunderland fans, it's unreal.
"Honestly, it's just unbelievable.
"It's massive for us.
"The manager just told me to play my game, get on the ball and make things happen.
"The space opened up for me, I’ve hit it and fortunately for me it's wobbled all over and gone in."